Genomic investigation of atypical malaria cases in Kanel, northern Senegal

Abstract

Background: The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools.

Methods: Malaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens.

Results: Nine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing.

Conclusions: This work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.

Keywords: Genetic surveillance; Infectious disease; Investigation; Metagenomic sequencing; Plasmodium falciparum; Serology.

Fig. 1

Timeline of Kanel malaria cases, September 2018

Fig. 2

Malaria Incidence Map in 2018 (Source NMCP), showing the location of the region of Matam, the district of Kanel and the village affected by the outbreak and the different health centers. Performed with QGIS 3.4.7 (http://www.qgis.osgeo.org)

Fig. 3

P. falciparum rapid diagnostic test (RDT) performed by the local medical team and PET-PCR for malaria species-typing and 24 SNP molecular barcode results. “N” represents a mixed-allele call. “M/P” genomic indicates monogenomic (M) or polygenomic (P) infections, based on the number of Ns; ≥ 2 represents a polygenomic infection. “X” represents a failed assay. H: House, f: female, m: male, M: monogenomic, P: polygenomic

Fig. 4

Antibody responses were detected by multiplex bead assay. A strong response to P. falciparum antigens (MSP1, CSP, LSA1, and GLURP) was observed. All virus antigens tested (CHKV, DENG.V2, DENG.V3, WNV, ZKV.VLP, YFV) were negative

Fig. 5

Phylogenetic tree shows the MT02 Pegivirus C (in red text) clustering with an African isolate from Ghana